SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Parsing and extracting from 2 Fasta Files Niranjanks Bioinformatics 1 01-12-2016 12:57 AM
extracting specific fasta sequences from whole genome file? ewhitt Bioinformatics 3 11-04-2015 11:18 AM
Extracting fasta sequence from bam file with bed intervals hin175 Bioinformatics 5 08-04-2015 08:44 AM
Extracting only the first match from FASTA file Henry_C Bioinformatics 4 06-01-2015 08:40 AM
Extracting 22-mers ending in GG from FASTA using sed/awk? Genomics101 Bioinformatics 6 09-16-2013 07:39 AM

Reply
 
Thread Tools
Old 08-17-2017, 09:06 AM   #1
Jane M
Senior Member
 
Location: Paris

Join Date: Aug 2011
Posts: 239
Question Extracting alternate loci from fasta genome

Dear all,

I downloaded full reference fasta genomes for hg19, mm9 and mm10 from gencode. They include reference chromosomes, scaffolds, assembly patches and haplotypes.
For a specific purpose, I want to remove haplotypes.
I did not manage to find a description of the nomenclature used for the contigs in fasta file.
In the hg19 reference genome I use, there are 297 contigs. One can see for example:
Quote:
>chr1 1
>chr2 2
...
>chrM MT
>GL877870.2 HG1007_PATCH
>GL877872.1 HG1032_PATCH
...
>GL383545.1 HSCHR10_1_CTG2 <- is it an "unlocalized sequence" ?
>GL383546.1 HSCHR10_1_CTG5
...
>GL000191.1 GL000191.1
>hg19GL000192.1 GL000192.1
I would like to know how many of them are haplotypes and which ones are they.
Is there a way to get this information?

Thank you in advance for your help.
Jane M is offline   Reply With Quote
Old 08-18-2017, 09:37 AM   #2
Jane M
Senior Member
 
Location: Paris

Join Date: Aug 2011
Posts: 239
Default

If it can help someone in the future, we can get this type of information on NCBI: ftp://ftp.ncbi.nlm.nih.gov/genomes/g...ate_mammalian/
In *_report.txt files, for each contigs, there is assembled-molecule / unlocalized-scaffold / unplaced-scaffold / novel-patch / fix-patch or alt-scaffold.
Jane M is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 02:49 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO